The genome sequence of the green-underside blue, Glaucopsyche alexis (Poda, 1761)

We present a genome assembly from an individual male Glaucopsyche alexis (the green-underside blue; Arthropoda; Insecta; Lepidoptera; Lycaenidae). The genome sequence is 620 megabases in span. The majority (99.87%) of the assembly is scaffolded into 23 chromosomal pseudomolecules, with the Z sex chromosome assembled.


Introduction
Glaucopsyche alexis is a species of the Polyommatinae subfamily (also known as the blues) found in temperate habitats from Northwestern Africa and Western Europe to Central Asia and Amur, including the Middle East and some Mediterranean islands. However, it is absent from several major islands, including the Balearic Islands, Sardinia, Crete, Cyprus and the Atlantic archipelago of Britain and Ireland (although a single specimen was recorded in Torquay, Devon, in September 1936). As with other Polyommatinae, adults exhibit a strong sexual dimorphism regarding the colour of the wing dorsal side: in males it is blue while, in females, it is predominantly brown. It is a univoltine species that overwinters as pupa. Adults fly during spring in most of its range, but they can fly until the beginning of summer in the coldest areas (Tshikolovets & Others, 2011). Caterpillars feed on a wide variety of Fabaceae; they are facultative myrmecophilous and tended by various ant taxa from the subfamilies Myrmicinae and Formicinae (Álvarez et al., 2012;Tolman & Lewington, 2008). This species has an overall stable population trend and it is listed as Least Concern in the IUCN Red List (van Swaay et al., 2013).

Genome sequence report
The male G. alexis specimen (Figure 1) was collected from Alcalá de la Selva, Teruel, Aragon, Spain (latitude 40.3638, longitude -0.7269). The genome was sequenced from a single male G. alexis to 43-fold coverage in Pacific Biosciences single-molecule long reads and 75-fold coverage in 10X Genomics read clouds. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 120 missing/misjoins and removed 21 haplotypic duplications, reducing the assembly size by 0.75% and scaffold number by 5.31%, and increasing the scaffold N50 by 7.99%. The final assembly has a total length of 620 Mb in 58 sequence scaffolds with a scaffold N50 of 27 Mb (Table 1). Of the assembly sequence, 99.87% was assigned to 23 chromosomal-level scaffolds, representing 22 autosomes (numbered by sequence length), and the Z sex chromosome (Figure 2- Figure 5; Table 2). The assembly has a BUSCO v5.1.2 (Simão et al., 2015) completeness of 97.1% (single 96.7%; duplicated 0.4%; fragmented 0.5%; missing 2.4%) using the lepidoptera_odb10 reference set (Table 1). While not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited. The mitochondrial genome was also assembled, with a total length of 15.2 kb.

Methods
The male G. alexis specimen was collected on 12 June 2019 using a net from Alcalá de la Selva, Teruel, Aragon, Spain (latitude 40.3638, longitude -0.7269) by Joan Carles Hinojosa (Institut de Biologia Evolutiva, Barcelona), and identified by Joan carles Hinojosa and Roger Vila (Institut de Biologia Evolutiva, Barcelona). The specimen was snap-frozen from live in liquid nitrogen.
DNA was extracted at the Tree of Life laboratory, WSI. The ilGlaAlex1 sample was weighed and dissected on dry ice with tissue set aside for Hi-C sequencing. Tissue from the whole organism was disrupted to a fine powder using a powermasher. Fragment size analysis of 0.01-0.5 ng of DNA was then performed using an Agilent FemtoPulse. High molecular weight (HMW) DNA was extracted using the Qiagen MagAttract HMW DNA extraction kit. Low molecular weight DNA was removed from a 200-ng aliquot of extracted DNA using 0.8X AMpure XP purification kit prior to 10X Chromium sequencing; a minimum of 50 ng DNA was submitted for 10X sequencing. HMW DNA was sheared into an average fragment size between 12-20 kb in a Megaruptor 3 system with speed setting 30. Sheared DNA was purified by solid-phase reversible immobilisation using AMPure PB beads with a 1.8X ratio of beads to sample to remove the shorter fragments and concentrate the DNA sample. The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer and Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the FemtoPulse system.
Pacific Biosciences HiFi circular consensus and 10X Genomics read cloud DNA sequencing libraries were constructed according to the manufacturers' instructions. DNA sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences SEQUEL II and Illumina HiSeq X instruments. Hi-C data were generated from abdomen tissue using the Arima v2.0 kit and sequenced on HiSeq X.
Assembly was carried out with HiCanu (Nurk et al., 2020); haplotypic duplication was identified and removed with purge_dups (Guan et al., 2020). One round of polishing was performed by aligning 10X Genomics read data to the assembly with longranger align, calling variants with freebayes (Garrison & Marth, 2012). The assembly was then scaffolded with Hi-C data (Rao et al., 2014) using SALSA2 (Ghurye et al., 2019. The assembly was checked for contamination and corrected using the gEVAL system (Chow et al., 2016) as described previously (Howe et al., 2021). Manual curation was performed using gEVAL, HiGlass (Kerpedjiev et al., 2018) and Pretext. The mitochondrial genome was assembled using Mito-HiFi (Uliano-Silva et al., 2021). The genome was analysed and BUSCO scores generated within the BlobToolKit environment (Challis et al., 2020). Table 3 contains a list of all software tool versions used, where appropriate. Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use. The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible.